Fluorescence imaging systems are regularly characterized by their ability to distinguish varying concentrations of fluorophores in a solution or tissue phantom. However, there is inadequate standardization in the field for fluorescence characterization. In this study, we characterize a fluorescence imaging system developed for pathogen detection, regarding its ability to detect a near-infrared dye. During this process, we vary a number of key factors involved in fluorescence imaging, such as the excitation intensity, background level, working distance, volume of fluorescent solution, and type of container used to hold the fluorescent solution. We then analyze the results, with statistical rigor, to determine which factors result in significant changes in fluorescence detection. Notably, we found that using different types of containers to hold the dye solution can have a significant impact on fluorescence detection, while the effects of working distance and excitation intensity can vary. Based on our findings, greater standardization, or at least more thorough reporting of the experimental setup, is recommended to researchers when publishing characterization results of new imaging systems.